//! (static)
Object* JSON::parseJSON(const std::string &s){
Tokenizer t;
Tokenizer::tokenList tokens;
t.getTokens(s.c_str(),tokens);
Tokenizer::tokenList::iterator it=tokens.begin();
Object * result= _parseJSON(it,tokens.end());
if(it!=tokens.end() && !Token::isA<TEndScript>(*it)){
std::cout << "JSON Syntax Error\n";
}
if(result==NULL){
result=String::create(s);
}
// for(it=tokens.begin();it!=tokens.end();++it){
// Token::removeReference(*it);
// }
return result;
}
int main(int ac, char* av[]) {
std::string str("");
for(int i=1; i<ac; i++)
str += av[i];
std::cout << "str: '" << str << "'\n";
std::deque<Token> tok;
Tokenizer tokenizer;
tok = tokenizer.getTokens(str);
std::cout << "tok.size() = " << tok.size() << "\n";
for (auto it = tok.begin(); it != tok.end(); it++)
(*it).dump();
return EXIT_SUCCESS;
}
void RPedigree::inputPed(string fileString){
// Authors: Rohan L. Fernando
// (2005)
// Contributors:
const char* fname = fileString.c_str();
cout << "reading pedigree file \n";
if (colName.size() < 3) {
cerr << "RPedigree::input(): colName.size() < 3 \n";
cerr << "Did you forget the putColNames method? \n";
throw exception("Error in RPedigree::input()");
}
int indIndex = colName.getIndex("individual");
if (indIndex == -1){
cerr << "RPedigree::input(): individual column is missing in colName \n";
throw exception("Error in RPedigree::input()");
}
int sireIndex = colName.getIndex("sire");
if (sireIndex == -1){
cerr << "RPedigree::input(): sire column is missing in colName \n";
throw exception("Error in RPedigree::input()");
}
int damIndex = colName.getIndex("dam");
if (damIndex == -1){
cerr << "RPedigree::input(): dam column is missing in colName \n";
throw exception("Error in RPedigree::input()");
}
unsigned numCol = colName.size();
double rec = 0, rec1 = 0;
string indstr, sirestr, damstr;
ifstream datafile(fname);
if(!datafile){
cout<< "Cannot open pedigree file: " << fname << endl;
exit(1);
}
datafile.setf(ios::skipws);
PNode *ptr;
std::string sep(" \t,\n\r");
std::string inputStr;
Tokenizer colData;
unsigned COUNT = 0;
while ( getline(datafile,inputStr) ){
colData.getTokens(inputStr,sep);
indstr = colData[indIndex];
sirestr = colData[sireIndex];
damstr = colData[damIndex];
rec++;
if(rec==1000){
cout<<rec+rec1<<"\r";
cout.flush();
rec1 += rec;
rec = 0;
}
if (colData.size() != numCol){
cerr << " Record " << rec1 + rec << " has " << colData.size() << " columns \n";
cerr << " Expected " << numCol << endl;
throw exception("Error in RPedigree::input()");
}
ptr = new PNode(indstr, sirestr, damstr);
if (orderedPed) ptr->ind = ++COUNT;
(*this)[indstr] = ptr;
}
datafile.close();
if(orderedPed){
seqnPed();
}
else {
generateEntriesforParents();
codePed();
}
makePedVector();
calc_inbreeding();
fillCoder();
}
